Genome Prairie

2018 Large-Scale Applied Research Project Competition

Request for Applications

2018 Large-Scale Applied Research Project Competition:

Genomics Solutions for Agriculture, Agri-food, Fisheries and Aquaculture

Request For Application (PDF)

Pre-Application Form (.docx)

Registration Form (.docx)

Registration Form - Appendix I (.xlsx)

Pre-Application Form - Appendix I (.xlsx)

 

Contacts:

Simon Potter (Manitoba proposals) - spotter@genomeprairie.ca; (204) 230-7974

Doug Heath (Saskatchewan proposals) - dheath@genomeprairie.ca; (306) 229-3658

 

1. Overview

The agriculture/agri-food and fisheries/aquaculture sectors are currently facing many challenges. The effects of climate change, such as severe weather extremes, shifting habitats, and pest and disease outbreaks are threatening agricultural production and quality. Consumer demand for products from non-conventional agricultural systems is increasing costs and lowering production volume, and regulatory challenges and uncertainties are hindering innovation and the adoption of new technologies. Capture fisheries are subject to drastic changes in availability, while aquaculture is the fastest growing food production sector in the world. Consequently, these sectors must find strategies to increase production efficiency, quality, and sustainability, while maintaining healthy ecosystems and providing safe products.  In addition, societal acceptance of genomics-based technologies is a major challenge faced by these sectors.

Canada is uniquely positioned to address many of these challenges. The agriculture/agri-food sector is considered to be one of the foundations of Canada’s economy, accounting for $111.9 billion of gross domestic product (GDP), about 8%, and employing 2.3 million people in 2016[1]. Canada is also a major exporter of key foodstuffs needed for global food security, producing 2% of the world’s cereals, and 3.4% of global oilseeds and pulses. The fisheries and aquaculture sector contributes $14.7 billion to the Canadian economy each year, and supports 130,000 jobs.[2] On a global scale, Canada is the steward of 25% of the world’s coastline and contributes 1% of the world’s fisheries production. Between 2011 and 2021, global fish consumption is projected to increase by 16%, with aquaculture expected to address the bulk of this increase. Finding sustainable solutions to these challenges will drive growth, productivity, commercialization and global competitiveness, offering significant benefit to Canada and the Canadian economy.

The agriculture/agri-food and fisheries/aquaculture sectors have a history of using research to assess challenges and develop solutions. In the genomics era, emerging knowledge and innovation have the potential to provide new approaches that can improve disease and pest resistance in our crops, livestock, and fish, increase our understanding of soil and aquatic microbiomes, improve early disease detection in livestock, and improve our ability to track, monitor and assess wild fish populations. Genomics-based approaches also have the potential to predict and mitigate the effects of climate change, such as understanding the response of fisheries to climate fluctuations, identifying crops and livestock that are more resilient to temperature extremes, and by reducing methane emissions related to livestock production systems.

Building upon regional stakeholder consultations across Canada and the resulting agriculture/agri-food and fisheries/aquaculture sector strategies, Genome Canada, together with Agriculture and Agri-Food Canada (AAFC), is seeking proposals for large-scale research projects which focus on the application of genomics[3]  in the agriculture/agri-food and fisheries/aquaculture sectors to address challenges and opportunities of importance to Canada[4],[5],[6]. The role of the agriculture and agri-food sector,[5] as well as the fisheries and aquaculture sector,[6] is well recognized for Canada’s economic growth and culture. Genomics will continue to be essential for the success of these sectors, contributing to Canada’s growing bioeconomy and the well-being of Canadians.

This funding opportunity builds on the complementary mandates of Genome Canada and AAFC and provides an opportunity to bring together and maximize the effectiveness of the research communities, infrastructure, and resources supported by both organizations. This funding opportunity makes it possible to collaboratively carry out joint projects with AAFC researchers, where Genome Canada funds will support the Genome Canada eligible researchers and AAFC funds will support the AAFC researchers.

2. Objective

The 2018 Large-Scale Applied Research Project Competition aims to support projects that will demonstrate how genomics research can be translated into solutions that advance the sustainability, productive capacity and the resulting competitive position of the Canadian agriculture/agri-food and fisheries/aquaculture sectors, and thereby contribute to the Canadian bioeconomy and the well-being of Canadians.

Applicants must demonstrate how their proposal will produce concrete deliverables by the end of the funding period that have the potential to be subsequently translated into significant social and/or economic benefits within as short a time-frame as possible after the end of the project.

To ensure that the objectives of the Request for Applications (RFA) are met, all applications will be evaluated according to the criteria established for the competition: 1) quality of the research proposal; 2) benefits for Canada; and, 3) management and financial aspects (see Appendix 1).

3. Funding Available and Term

4. Research into the implications of genomics in society (GE3LS research[7])

While genomics and its applications have the potential to have significant social and economic impact in the agriculture/agri-food and fisheries/aquaculture sectors, there remain potential barriers to the acceptance and uptake of the outcomes from this research. To help promote the use of genomic-based research and innovation, this competition supports research into the implications of genomics in society (GE3LS research). Specifically, such research is intended to investigate key factors that may facilitate or hinder the effective translation of research, and the uptake of genomic-based applications. 

GE3LS research may be conducted by researchers from universities, government, industry, not-for-profit or other organizations, who generally are trained in disciplines other than the life sciences, including social or behavioural scientists or humanities scholars. Such GE3LS research may be conducted in two forms:

Following the funding decisions on this competition, Genome Canada will determine if additional mechanisms are required to maximize the GE3LS research and the overall social and/or economic benefits that can be realized through this competition. For example, to the extent that integrated GE3LS research across different projects and/or stand-alone GE3LS research projects are addressing the same research area, are focused on the same overarching objectives, or are using similar research approaches, additional support may become available to achieve greater impact through the coordination and strengthening of collaborations between researchers, users and other stakeholders, thereby accelerating the translation of research and the responsible uptake of genomic-based applications in the sectors relevant to this competition.

5. Eligibility of Proposals

To be eligible for this competition, proposals must:

To be eligible for AAFC funding, applicants must satisfy the requirements for the competition as outlined above as well as any additional requirements put forth by AAFC as described in Appendix 2.

This RFA provides an opportunity for research teams to propose large-scale projects that would be part of even larger national and international research initiatives, as long as the eligibility criteria are met.

Projects funded through this competition must focus on using genomic approaches to address challenges and opportunities of importance to Canada’s agriculture/agri-food and/or fisheries/aquaculture sectors. Topics of applied research that could be addressed include, but are not limited to, the following:

NOTE: Studies focussing on genomics related to companion animals are not eligible for support in this competition.Eligible animal species for study must be part of agriculture or aquaculture food production systems or the wild commercial fishery. Studies focussed on companion animals may, however, be able to obtain support from other Genome Canada programs such as the Genomic Applications Partnership Program depending on the details of the proposal and whether it meets the eligibility criteria of these other programs.

Integrated GE3LS research topics that could be addressed in this competition include, but are not limited to, the following:

In order to maximize the effectiveness of this RFA in advancing genomics research and its application in Canada, rapid sharing of the outputs of the research (e.g., publications, data and resources) is required (see Genome Canada’s Data Release and Sharing Policies).

6. User Engagement

All projects must clearly demonstrate engagement with users in the development and execution of the research plan in order to help ensure receptor uptake and practical applicability of the research. For the purpose of large-scale genomics projects with integrated GE3LS research, this engagement should inform the genomics research, the GE3LS research, and to the extent possible, its integration into the overall project.

 “Users” in the context of this RFA can be defined as those who are able to use the information generated through research to make informed decisions on relevant issues, policies, programs and product development. Examples of user organizations could include industry and industry associations, producer organizations, government departments and regulatory agencies. Individuals from these types of organizations should be included on the project team.

Users must be clearly integrated into the project team in the form of a project team member, collaborator and/or member of the management team. Users are encouraged to actively collaborate in the priority setting and conduct of research as well as in summarizing, distributing, sharing, and applying its resulting knowledge. Co-funding would clearly demonstrate user interest in the project’s potential deliverables, although it is not a requirement for a user organization to contribute to the co-funding required.

7. Benefits for Canada

All applications must describe, with supporting evidence, the concrete deliverable(s) that will be realized by the end of the project that have the potential for subsequent translation into significant social and/or economic benefits for Canada.

Proposals that make a strong case that the project deliverables can and will be translated into significant social and/or economic benefits within as short a time-frame as possible after the end of the project are particularly encouraged, taking into consideration what is reasonable for the proposed deliverables.

Applications must include a plan which explains the next steps of how the deliverables from the research will be transferred, disseminated, used, and/or applied to realize the social and/or economic benefits.  Once funded, the project teams will be required to further elaborate on the path forward to ensure that the proposed deliverables are realized in the stated timeframe and within the approved budget.  The project’s Research Oversight Committee (see 10.2) will assess the plan on an on-going basis.

8. Competition Timeline

Applications must be submitted to Genome Canada through Genome Prairie. The competition timeline outlined below includes Genome Canada’s deadlines. Please contact your Genome Centre for further information on their process and internal deadline dates, as these could be a month or more earlier than the Genome Canada deadline for certain steps of the competition.

June 2018

Launch of competition

August 10, 2018

Deadline for submitting registrations to Genome Prairie

November 15, 2018

Deadline for submitting pre-applications to Genome Canada

Late January 2019

Applicants notified of results of pre-application 

April 11, 2019

Deadline for full applications to Genome Canada

Late May, 2019

Review committee meets (including meetings with applicants)

Late June 2019

Decisions by Genome Canada and AAFC

Late June 2019

Notification of Decision

 

9. Application Process

Applicants are required to apply for funding through their regional Genome Centre.  The application process is comprised of three steps: Registration, Pre-Application and Full Application.

9.1.Registration

A brief Registration form will be used to provide early guidance on elements such as who is applying, what they are planning to do, research areas including integrated GE3LS, expected deliverables, approximate budgets and suggested reviewers. This allows for screening of eligibility by the Genome Centres and facilitates the early selection of reviewers for the peer review process.  Information from eligible registrations (i.e., name of project leader(s), lead institution, title of project, research areas and keywords) will be posted on the Genome Canada website to facilitate the identification of areas of potential synergy between applications across the country, so that applicants can consider engaging with other researchers on a common project. This will also make possible the exchange of required information between project teams and genomics technology service providers, such as Genome Canada supported Genomics Technology Platforms.

9.2. Pre-Application

For the Pre-Application, applicants will be asked to submit a short description of the following:

Also, please see Appendix 2 for additional requirements at the Pre-Application stage for applications requesting AAFC funding.

Pre-Applications will be reviewed in a two-stage process. The first stage involves an initial review that will be done “at-home” by a College of Reviewers who will evaluate the Pre-Applications, focusing on the quality of the research plan and the potential for benefits for Canada. College reviews will provide a rating for the quality of the research proposal and potential for benefits, and the mean score for each of these categories will be calculated separately.  A ranking list of the Pre-Applications, based upon the mean of the scores for both criteria (quality of the research proposal and benefits) will be prepared. The Pre-Applications with the lowest scores will not be considered further.      

The second stage will involve review by a Pre-Application Review Committee (PARC) with broad expertise in research including GE3LS, technology development, research management and the translation of research results in areas relevant to the competition. This committee will consider the College reviews and make a final recommendation to Genome Canada on which Pre-Applications should be invited to submit a Full Application.

The proposals will again be checked for eligibility to the program. Only the most competitive Pre-Applications will be invited to submit full applications. Information from approved Pre-Applications (i.e., name of project leader(s), lead institution, title of project, research areas and keywords) will be posted on the Genome Canada website to further facilitate the exchange of information between project teams and genomics technology service providers such as the Genome Canada supported Genomics Technology Platforms.

9.3. Full Application

Those applicants successful at the Pre-Application stage will be asked to submit a full application. Full applications must address the evaluation criteria established for the competition, i.e., 1) quality of the research project; 2) benefits for Canada; and, 3) management and financial aspects. A final check for eligibility will be carried out. A multidisciplinary committee of experts, with expertise in assessing all of the review criteria, will be established to review applications. The review committee will meet with and interview representatives from each project through a face-to-face meeting.  After the review committee completes its deliberations and develops an overall ranking list, it will provide its recommendations to Genome Canada and AAFC, who have the final authority for funding decisions.

The evaluation processes may be adjusted where warranted by the complexity of proposals received or other relevant factors.Any changes will be communicated through Genome Canada’s website and through the Genome Centres.

See Appendix 2 for additional requirements at the full application stage for applications requesting AAFC funding.

10. Project Management and Oversight

10.1. Project Managers

All approved projects must have a dedicated project manager. Project managers coordinate administrative and reporting requirements and support the project’s research enterprise.

10.2. Research Oversight Committees

All Genome Canada funded projects will have a Research Oversight Committee (ROC) constituted by, and reporting to, the Genome Centre(s). The ROC reports to the Genome Centre on the progress being made by the project and makes recommendations to the funders regarding continued funding, as well as providing advice and guidance to the research team to help ensure that the project achieves its stated objectives and milestones.The membership of the ROC must be completely independent from the project, with no real or perceived conflicts of interest and should be composed of experts who will work with the Genome Centre and the funders to maximize the successful outcomes of the project.A portion of the funds awarded to each project will be designated to cover costs associated with the project's ROC.

11. Co-Funding

A project’s eligible costs must be co-funded from eligible sources (other than the AAFC funds designated as part of the collaboration) such that the co-funding is at least equal to the Genome Canada contribution. The Genome Centres, working with the applicants, are responsible for securing co-funding. Co-funding for this competition must be for research activities that are an integral part of the Genome Canada approved project and must be for eligible costs specifically requested in the Genome Canada budget form. See the Guidelines for Funding  for more details.

12. Communication and Outreach

Public communication and outreach are important activities to help advance scientific knowledge and understanding. Public understanding of science benefits both the public and scientific communities as well as helping influence governmental decision making with regard to regulation, science policy and funding. Project teams are encouraged to work with their stakeholders, Genome Centres and other groups to communicate the outputs of their research to a broad community.

13. Contacts

Andy Stone

Genome Atlantic

astone@genomeatlantic.ca

902-421-5645

B.F. Francis Ouellette     

Genome Québec

LSARP2018@genomequebec.com          

514 398-0668 x 203

Caitlin Taylor

Ontario Genomics

ctaylor@ontariogenomics.ca

416-673-6512 

Simon Potter

Genome Prairie

spotter@genomeprairie.ca

204-230-7974

Niall Kerrigan

Genome Alberta 

nkerrigan@genomealberta.ca

403-210-5252

Lisey Mascarenhas

Genome British

Columbia

lmascarenhas@genomebc.ca

604- 637-3087

 

Appendix 1. Evaluation Criteria

Proposals submitted to Genome Canada are evaluated via a rigorous independent peer review process to assess their research merit and potential for social and/or economic benefits for Canada, as well as to ensure that sound management and financial practices are implemented.

Eligibility Criteria

Each proposal will be reviewed for eligibility at each stage of the application process. The following criteria will be used:

If considered eligible, the proposal will be reviewed using the criteria described below:

The review criteria fall into three categories:

1)          Research Proposal;
2)          Benefits for Canada; and,
3)          Management and Finance

Note that the descriptive phrases which follow the criteria below are not all-inclusive.

1. Research Proposal

Including research into the implications of genomics in society (GE3LS research)

2. Benefits for Canada

3. Management and Finance

Appendix 2.  Strategic Collaboration with Agriculture and Agri-Food Canada (AAFC)

Description

Genome Canada and AAFC will jointly support research projects developing genomic solutions for challenges and opportunities in the agriculture and agri-food sector through Genome Canada’s 2018 Large-Scale Applied Research Project Competition.  This funding opportunity builds on the complementary mandates of Genome Canada and AAFC and provides an opportunity to bring together and maximize the effectiveness of the research communities, infrastructure and resources supported by both organizations. This funding opportunity makes it possible to collaboratively carry out joint projects with AAFC researchers, where Genome Canada funds will support the Genome Canada eligible researchers and AAFC funds will support the AAFC researchers.

Background

Agriculture and Agri-Food Canada provides research, development and technology transfer (RDT) capacity to serve producers, processors, industry and Canadians by approaching all of their challenges and opportunities (agronomic, economic and environmental) in the same integrated way they do when they run their businesses.

AAFC RDT capacity is located in 20 research and development centres and in sub-stations throughout Canada.  AAFC scientists, technicians and staff work to create better opportunities for farmers and all Canadians through agricultural research and innovation.

AAFC has been at the forefront of agricultural genomics-based innovation in Canada. This leadership was enabled by a number of federal investments, such as the Genomics Research and Development Initiative (GRDI), the series of Agriculture Policy Frameworks (currently entitled Canadian Agricultural Partnership), and from Budget 2016 (to support genomics, digitization and data mobilization of AAFC’s biological collections).  Key strategic areas of investment included cereals, oilseeds, pulses, as well as foundational activities towards national biodiversity collections and bioinformatics. 

Funds Available

Eligible Research Areas for AAFC Funding

Based on internal consultations (2016, 2018) and the results from the transformative workshops, AAFC investments in Collaborative Projects will focus in the following areas:

Process (for AAFC portion of Collaborative Projects only) 

 

[3] The term genomics is defined here as the comprehensive study, using high throughput technologies, of the genetic information of a cell or organism and its functions. The definition also includes related disciplines such as epigenomics, metabolomics, metagenomics, proteomics, transcriptomics, bioinformatics and synthetic biology as long as the link to genetic information is clear.

[4] The Opportunity for Agri-Food Genomics in Canada: Ours for the making. May 2013 https://www.genomecanada.ca/sites/default/files/agri_food_en.pdf

[5] Genomics for Agriculture and Agri-Food: Canada’s strategic opportunity. Summary of the regional consultations, June-September 2017

[6] Canadian Fisheries and Aquaculture: How genomics can address sector challenges. August 2013 https://www.genomecanada.ca/sites/default/files/fisheries_and_aquaculture_en.pdf

[7] The acronym GE3LS stands for “Genomics and its Ethical, Environmental, Economic, Legal and Social aspects”.  However, it should be understood broadly as research into the implications of genomics in society from the perspective of the social sciences and humanities. Therefore, it is not strictly limited to disciplines that make-up the acronym but rather encompasses all those that rely on quantitative and qualitative methodologies to investigate the implications of genomics in society, and inform applications, practices and policies. In the context of this RFA, it can also include approaches from a wide range of disciplines including but not limited to: development studies, environmental sciences, food studies, geography, innovation studies, political sciences and population studies.